Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.

Wei Chen,Silvas J Prince,Yongqiang C An,Rupesh K Deshmukh,Babu Valliyodan,Gaurav Agarwal,Yongqin Wang,Qiuming Yao,Biao Wang,Dong Xu,Henry T Nguyen,Gunvant B Patil,Li Lin,Rajeev K Varshney,Li Song

doi:10.3389/fpls.2016.01044

Abstract

Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2724 and 3498 DEGs were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.

Highlights

Soybeans, the most important legume crop worldwide, are an essential source of oil and protein for humans and livestock, and are considered a potential source of bio-diesel (Koberg et al, 2011)
Plant responses toward abiotic stress are complex and involve several different mechanisms regulated by crosstalk between genes related to hormonal signaling, photosynthesis, respiration, and transcriptional regulations
Comparative transcriptome profiling performed in this study under drought and flooding has provided an opportunity to evaluate the categorized molecular responses

Summary

Introduction

The most important legume crop worldwide, are an essential source of oil and protein for humans and livestock, and are considered a potential source of bio-diesel (Koberg et al, 2011). Considering the importance of soybeans for food and nutritional security, there have been extensive efforts toward increasing soybean production. Soybean yield improvement is facing severe challenges and suffers with yield loss due to a range of biotic and abiotic stresses. Extreme water regimes such as drought and flooding cause severe yield losses in all major crops including soybeans, rice, corn, and wheat (Perata et al, 2011). Flooding is caused by heavy rainfall and results in water logging and submergence. In soybeans, both drought and flooding can cause up to a 40–60% yield loss worldwide (Valliyodan and Nguyen, 2006; Komatsu et al, 2009; Ahmed et al, 2013)

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